GlyCombo enables rapid, complete glycan composition identification across diverse glycomic sample types

13 August 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Glycans are sugar-based polymers found to modify biomolecules including lipids and proteins, as well as occur unconjugated as free polysaccharides. Due to their ubiquitous cellular presentation, glycans mediate crucial biological processes and are frequently sought after as biomarkers for a wide range of diseases. Identification of glycans present in samples acquired with mass spectrometry (MS) is a cornerstone of glycomics research, thus, the ability to rapidly identify glycans in each acquisition is integral to glycomics analysis pipelines. Here we introduce GlyCombo (https://github.com/Protea-Glycosciences/GlyCombo), an open-source, freely available software tool designed to rapidly assign monosaccharide combinations to glycan precursor masses including those subjected to MS2 in LC-MS/MS experiments. GlyCombo was evaluated across six diverse datasets, demonstrating MS vendor, derivatization, and glycan-type neutrality. Compositional assignments using GlyCombo are shown to be faster than the current, predominant approach, GlycoMod, a closed-source web application. Two unique features of GlyCombo, multiple adduct search and off-by-one error anticipation, reduced unassigned MS2 scans in a benchmark dataset by 40%. Finally, the comprehensiveness of glycan feature identification is exhibited in Skyline, a software that requires pre-defined transitions that are derived from GlyCombo output files.

Keywords

glycomics
glycoinformatics
LCMS

Supplementary materials

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Description
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Supplementary table with raw values for figures
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Excel spreadsheet containing glycan preset numbers, search times for GlyCombo, composition identification rates across datasets, and MS2 scan annotations corresponding to GlyCombo features
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Supplementary figures and tables
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Supplementary tables and figures associated with the manuscript: Feature comparison between GlycoMod and Glycombo, example Skyline output file from GlyCombo, simplified GlyCombo process by recursive loop memoisation, and the GlyCombo recursive tree framework structure to prevent recursive composition calculations.
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Supplementary weblinks

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